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Started by upstream project "BIOFORMATS-test-repo" build number 92 originally caused by: Started by upstream project "Trigger" build number 103 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins14603780423452663203.sh + '[' zip = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_14099_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 01:22:52,975 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:52,977 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:22:52,977 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:52,979 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:52,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:52,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:52,979 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:22:52,979 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:52,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:52,980 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:52,980 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:52,980 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:53,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:53,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:53,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:53,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:53,265 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:53,265 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:53,265 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:53,265 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:53,265 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:22:53,266 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:22:53,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 286 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-14 01:22:53,276] [main] java.version = 1.8.0_342 [testng] 01:22:53,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:53,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-14_01-22-53.log] [testng] 01:22:53,328 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-14 01:22:53,330] [main] testng.directory = /data [testng] [2024-06-14 01:22:53,330] [main] testng.configDirectory = /config [testng] [2024-06-14 01:22:53,343] [main] testng.multiplier = 1.0 [testng] [2024-06-14 01:22:53,343] [main] testng.in-memory = false [testng] [2024-06-14 01:22:53,343] [main] testng.allow-missing = false [testng] [2024-06-14 01:22:53,343] [main] user.language = en [testng] [2024-06-14 01:22:53,343] [main] user.country = ${user.country} [testng] [2024-06-14 01:22:53,344] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-14 01:22:53,817] [main] ---------------------------------------- [testng] [2024-06-14 01:22:53,817] [main] Total files: 22 [testng] [2024-06-14 01:22:53,817] [main] Scan time: 0.473 s (21 ms/file) [testng] [2024-06-14 01:22:53,817] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-14 01:23:42,365] [pool-1-thread-1] Initializing /data/imagej/3D_Chromosome.zip: [testng] 01:23:42,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:42,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,367 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-14_01-23-42.log] [testng] 01:23:42,367 |-INFO in ch.qos.logback.core.sift.SiftProcessor@322b18ab - End of configuration. [testng] [2024-06-14 01:23:42,720] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] 01:23:42,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:42,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-14_01-23-42.log] [testng] 01:23:42,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2695e169 - End of configuration. [testng] [2024-06-14 01:23:42,827] [pool-1-thread-11] Initializing /data/imagej/scala-media.zip: [testng] 01:23:42,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:42,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-14_01-23-42.log] [testng] 01:23:42,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce7b1f1 - End of configuration. [testng] [2024-06-14 01:23:42,933] [pool-1-thread-10] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 01:23:42,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:42,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,934 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-14_01-23-42.log] [testng] 01:23:42,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@587038af - End of configuration. [testng] [2024-06-14 01:23:43,171] [pool-1-thread-9] Initializing /data/imagej/mri-stack.zip: [testng] 01:23:43,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:43,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:43,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-14_01-23-43.log] [testng] 01:23:43,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77574f08 - End of configuration. [testng] [2024-06-14 01:23:43,416] [pool-1-thread-8] Initializing /data/imagej/blood-brain-barrier.zip: [testng] 01:23:43,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:43,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:43,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-14_01-23-43.log] [testng] 01:23:43,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f44bb33 - End of configuration. [testng] [2024-06-14 01:23:48,814] [pool-1-thread-7] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:23:48,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:48,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-14_01-23-48.log] [testng] 01:23:48,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e5d4bdc - End of configuration. [testng] [2024-06-14 01:23:49,930] [pool-1-thread-6] Initializing /data/imagej/m51.zip: [testng] 01:23:49,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:49,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-14_01-23-49.log] [testng] 01:23:49,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e62f409 - End of configuration. [testng] [2024-06-14 01:23:50,019] [pool-1-thread-5] Initializing /data/imagej/se3.zip: [testng] 01:23:50,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:50,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:50,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-14_01-23-50.log] [testng] 01:23:50,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cbc2aec - End of configuration. [testng] [2024-06-14 01:23:53,877] [pool-1-thread-4] Initializing /data/imagej/hela-cells.zip: [testng] 01:23:53,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:53,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:53,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-14_01-23-53.log] [testng] 01:23:53,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dee9026 - End of configuration. [testng] [2024-06-14 01:23:54,605] [pool-1-thread-3] Initializing /data/imagej/FluorescentCells.zip: [testng] 01:23:54,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:54,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:54,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-14_01-23-54.log] [testng] 01:23:54,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4825fcbf - End of configuration. [testng] [2024-06-14 01:23:54,788] [pool-1-thread-2] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 01:23:54,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:54,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:54,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-14_01-23-54.log] [testng] 01:23:54,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20c81910 - End of configuration. [testng] [2024-06-14 01:24:02,529] [pool-1-thread-11] Initializing /data/samples/sdub.zip: [testng] [2024-06-14 01:24:02,996] [pool-1-thread-6] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-06-14 01:24:04,712] [pool-1-thread-12] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-06-14 01:24:12,771] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-06-14 01:24:14,568] [pool-1-thread-3] Initializing /data/imagej/RatBrain.zip: [testng] [2024-06-14 01:24:15,258] [pool-1-thread-9] Initializing /data/imagej/fat-cells.zip: [testng] [2024-06-14 01:24:19,596] [pool-1-thread-1] Initializing /data/imagej/flybrain.zip: [testng] [2024-06-14 01:24:26,057] [pool-1-thread-11] Initializing /data/imagej/xrays.zip: [testng] [2024-06-14 01:24:26,647] [pool-1-thread-3] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-06-14 01:24:29,699] [pool-1-thread-11] Initializing /data/imagej/confocal-series.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 39 seconds Finished: SUCCESS